Alignments for a candidate for bamE in Geobacter metallireducens GS-15

GapMind for catabolism of small carbon sources

Alignments for a candidate for bamE in Geobacter metallireducens GS-15

Align Polyferredoxin, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate WP_011365914.1 GMET_RS10510 CoB--CoM heterodisulfide reductase iron-sulfur subunit A family protein

Query= uniprot:Q39TW1
         (1014 letters)



>NCBI__GCF_000012925.1:WP_011365914.1
          Length = 1014

 Score = 2056 bits (5327), Expect = 0.0
 Identities = 1014/1014 (100%), Positives = 1014/1014 (100%)

Query: 1    MNTSDRNIGDVLIVGGGISGIQAALDLANSGFRVFLVDKSPALGGKMSQLDKTFPTNDCS 60
            MNTSDRNIGDVLIVGGGISGIQAALDLANSGFRVFLVDKSPALGGKMSQLDKTFPTNDCS
Sbjct: 1    MNTSDRNIGDVLIVGGGISGIQAALDLANSGFRVFLVDKSPALGGKMSQLDKTFPTNDCS 60

Query: 61   MCIESPKFIECARNPNIEIITYTEVERVDGEAGDFRVTLTKKPRYISEEKCTGCNICVDY 120
            MCIESPKFIECARNPNIEIITYTEVERVDGEAGDFRVTLTKKPRYISEEKCTGCNICVDY
Sbjct: 61   MCIESPKFIECARNPNIEIITYTEVERVDGEAGDFRVTLTKKPRYISEEKCTGCNICVDY 120

Query: 121  CPVKIPDPFNQNLSENKAVHIYFSQAVPLVTYVDPETCLYLKEGKCQICVGACKTKAIDL 180
            CPVKIPDPFNQNLSENKAVHIYFSQAVPLVTYVDPETCLYLKEGKCQICVGACKTKAIDL
Sbjct: 121  CPVKIPDPFNQNLSENKAVHIYFSQAVPLVTYVDPETCLYLKEGKCQICVGACKTKAIDL 180

Query: 181  HQKPETMVVEVGAIILSPGYETFNPKLRGDFGYGRMQNVVTSLDFERILCATGPYEGEIL 240
            HQKPETMVVEVGAIILSPGYETFNPKLRGDFGYGRMQNVVTSLDFERILCATGPYEGEIL
Sbjct: 181  HQKPETMVVEVGAIILSPGYETFNPKLRGDFGYGRMQNVVTSLDFERILCATGPYEGEIL 240

Query: 241  RPSDKKHPHKIAWIQCVGSRQVNEGGNNYCSAVCCAYSQKQVILAKDHDADLQATIFHND 300
            RPSDKKHPHKIAWIQCVGSRQVNEGGNNYCSAVCCAYSQKQVILAKDHDADLQATIFHND
Sbjct: 241  RPSDKKHPHKIAWIQCVGSRQVNEGGNNYCSAVCCAYSQKQVILAKDHDADLQATIFHND 300

Query: 301  VRAYGKDFERFHQRAEKLSDVRFVRSYVTIGREIESTKNVTIRYSTVDDGVKEEEFDMVV 360
            VRAYGKDFERFHQRAEKLSDVRFVRSYVTIGREIESTKNVTIRYSTVDDGVKEEEFDMVV
Sbjct: 301  VRAYGKDFERFHQRAEKLSDVRFVRSYVTIGREIESTKNVTIRYSTVDDGVKEEEFDMVV 360

Query: 361  LSVGLNPPKDVEALASKIGIELTDQKFCKNNPYNPIETSRKGVFVSGAFQGPLDIPESVV 420
            LSVGLNPPKDVEALASKIGIELTDQKFCKNNPYNPIETSRKGVFVSGAFQGPLDIPESVV
Sbjct: 361  LSVGLNPPKDVEALASKIGIELTDQKFCKNNPYNPIETSRKGVFVSGAFQGPLDIPESVV 420

Query: 421  TASGAGALCGQLLSYRRGRLERERVYPPEKDVSQEELKIGVVVCYCGANIGRVVNIPEVI 480
            TASGAGALCGQLLSYRRGRLERERVYPPEKDVSQEELKIGVVVCYCGANIGRVVNIPEVI
Sbjct: 421  TASGAGALCGQLLSYRRGRLERERVYPPEKDVSQEELKIGVVVCYCGANIGRVVNIPEVI 480

Query: 481  EYAATLPNVAWAGENLFACSTENAKQISDAIVAKGLNRVVLAACTPRTHEPLFRDTCREA 540
            EYAATLPNVAWAGENLFACSTENAKQISDAIVAKGLNRVVLAACTPRTHEPLFRDTCREA
Sbjct: 481  EYAATLPNVAWAGENLFACSTENAKQISDAIVAKGLNRVVLAACTPRTHEPLFRDTCREA 540

Query: 541  GLNQYFFEFANIREHCSWVHSREKESATQKAKEIVRMSVARAAHLEPLQEFQLPVDHTGL 600
            GLNQYFFEFANIREHCSWVHSREKESATQKAKEIVRMSVARAAHLEPLQEFQLPVDHTGL
Sbjct: 541  GLNQYFFEFANIREHCSWVHSREKESATQKAKEIVRMSVARAAHLEPLQEFQLPVDHTGL 600

Query: 601  VVGGGVAGMTAALNMAEQGFEVYLIEKDDDLGGMARRLHYTLEGMDVQSFLADLVKKVYR 660
            VVGGGVAGMTAALNMAEQGFEVYLIEKDDDLGGMARRLHYTLEGMDVQSFLADLVKKVYR
Sbjct: 601  VVGGGVAGMTAALNMAEQGFEVYLIEKDDDLGGMARRLHYTLEGMDVQSFLADLVKKVYR 660

Query: 661  HPRVHVWTDANITDVSGYVGNFVTTVTSQGRNREVKHGVAVIATGAQEYKPTEYLYGESD 720
            HPRVHVWTDANITDVSGYVGNFVTTVTSQGRNREVKHGVAVIATGAQEYKPTEYLYGESD
Sbjct: 661  HPRVHVWTDANITDVSGYVGNFVTTVTSQGRNREVKHGVAVIATGAQEYKPTEYLYGESD 720

Query: 721  RVLTQLELEGEIVSQSEKVTGAQSVVMIQCVGCRQADRNYCSRVCCSQAIKNAHKLKEIN 780
            RVLTQLELEGEIVSQSEKVTGAQSVVMIQCVGCRQADRNYCSRVCCSQAIKNAHKLKEIN
Sbjct: 721  RVLTQLELEGEIVSQSEKVTGAQSVVMIQCVGCRQADRNYCSRVCCSQAIKNAHKLKEIN 780

Query: 781  PEMEIQIIFRDMRTYGLKETYYREASEKNVKFIRYEAETKPVVEAAGDGFKVTVPDPVLG 840
            PEMEIQIIFRDMRTYGLKETYYREASEKNVKFIRYEAETKPVVEAAGDGFKVTVPDPVLG
Sbjct: 781  PEMEIQIIFRDMRTYGLKETYYREASEKNVKFIRYEAETKPVVEAAGDGFKVTVPDPVLG 840

Query: 841  QMMELEADLVVLAAAVIPAESSQDAGKLFKVSNNPDGFFQEAHVKLRPVDFAADGVFLCG 900
            QMMELEADLVVLAAAVIPAESSQDAGKLFKVSNNPDGFFQEAHVKLRPVDFAADGVFLCG
Sbjct: 841  QMMELEADLVVLAAAVIPAESSQDAGKLFKVSNNPDGFFQEAHVKLRPVDFAADGVFLCG 900

Query: 901  TAHYPKHLSETISQAYGAAGRAVGILSRETVTASGAVCDVTESDCVSCGACITACKYGAI 960
            TAHYPKHLSETISQAYGAAGRAVGILSRETVTASGAVCDVTESDCVSCGACITACKYGAI
Sbjct: 901  TAHYPKHLSETISQAYGAAGRAVGILSRETVTASGAVCDVTESDCVSCGACITACKYGAI 960

Query: 961  SFVDTPNGKKARVEPILCKGDGLCNAKCPTGAIYLKHYTDDEICAQIDAAFPEH 1014
            SFVDTPNGKKARVEPILCKGDGLCNAKCPTGAIYLKHYTDDEICAQIDAAFPEH
Sbjct: 961  SFVDTPNGKKARVEPILCKGDGLCNAKCPTGAIYLKHYTDDEICAQIDAAFPEH 1014


Lambda     K      H
   0.319    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3324
Number of extensions: 138
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1014
Length of database: 1014
Length adjustment: 45
Effective length of query: 969
Effective length of database: 969
Effective search space:   938961
Effective search space used:   938961
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources